temperature salinity

00-scripts/sss.R

+###############################################################################
+## Librairies
+library("raster")
+library("rgdal")
+library("ncdf4")
+
+
+## load data
+coo=read.csv("01-sample_coords/all_coords.csv",sep="\t")
+coo=na.omit(coo)
+names(coo)=c("id","lat","lon")
+latlon = data.frame(lon=coo$lon,lat=coo$lat)
+coordinates(latlon) = c("lon", "lat")
+### indiquer que les lat/lon est en projection google map
+proj4string(latlon) = CRS("+init=epsg:4326")
+
+fichier="01-infos/salinity/MEDSEA_PHY_006_004_SSS_jan1987-nov2016_monthly.nc"
+br <- brick(fichier)
+##convertir les lat/lon dans la projection du raster "rp"
+latlon = spTransform(latlon,proj4string(br))
+
+buffer_distance=13000
+tt=extract(br,latlon, buffer=buffer_distance,fun=mean,normalizeWeights=FALSE,weigths=TRUE,factors=TRUE)
+
+january=tt[,seq(1,(359-10),12)]
+february=tt[,seq(2,(359-9),12)]
+march=tt[,seq(3,(359-8),12)]
+april=tt[,seq(4,(359-7),12)]
+may=tt[,seq(5,(359-6),12)]
+june=tt[,seq(6,(359-5),12)]
+july=tt[,seq(7,(359-4),12)]
+august=tt[,seq(8,(359-3),12)]
+september=tt[,seq(9,(359-2),12)]
+october=tt[,seq(10,(359-1),12)]
+november=tt[,seq(11,359,12)]
+december=tt[,seq(12,359-11,12)]
+
+year=list(january,february,march,april,may,june,july,august,september,october,november,december)
+
+
+
+monthlysalinity.frame <- as.data.frame(matrix(,ncol=(36),nrow=0))
+for(i in seq(1,dim(tt)[1])){
+ yeartemp=c()
+ for(mois in seq(1,12)) {
+  month_min=min(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
+  month_max=max(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
+  month_mean=mean(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
+  yeartemp=c(yeartemp,month_min,month_max,month_mean)
+ }
+ monthlysalinity.frame=rbind(monthlysalinity.frame,yeartemp) 
+}
+
+mois_nom=c("january","february","march","april","may","june","july","august","september","october","november","december")
+value_nom=c("min","max","mean")
+col_nom=c()
+for(m in mois_nom){
+	for(n in value_nom) {
+		mois_value=paste(m,n,sep="_")
+		nom_value=paste("SSS",as.character(mois_value),sep="_")
+		col_nom=c(col_nom,as.character(nom_value))
+	}
+}
+colnames(monthlysalinity.frame)=col_nom
+
+monthlysalinity.coo=cbind(coo,monthlysalinity.frame)
+
+write.table(monthlysalinity.coo, file="03-results/all_monthly_salinity.tsv",quote=F,sep="\t",col.names=T,row.names=F)
\ No newline at end of file

00-scripts/sst.R

+###############################################################################
+## Librairies
+library("raster")
+library("rgdal")
+library("ncdf4")
+
+## load data
+coo=read.csv("01-sample_coords/all_coords.csv",sep="\t")
+coo=na.omit(coo)
+names(coo)=c("id","lat","lon")
+latlon = data.frame(lon=coo$lon,lat=coo$lat)
+coordinates(latlon) = c("lon", "lat")
+### indiquer que les lat/lon est en projection google map
+proj4string(latlon) = CRS("+init=epsg:4326")
+
+
+
+fichier="01-infos/temperature/MEDSEA_PHY_006_004_SST_jan1987-nov2016_monthly.nc"
+br <- brick(fichier)
+##convertir les lat/lon dans la projection du raster "rp"
+latlon = spTransform(latlon,proj4string(br))
+
+buffer_distance=13000
+tt=extract(br,latlon, buffer=buffer_distance,fun=mean,normalizeWeights=FALSE,weigths=TRUE,factors=TRUE)
+
+
+january=tt[,seq(1,(359-10),12)]
+february=tt[,seq(2,(359-9),12)]
+march=tt[,seq(3,(359-8),12)]
+april=tt[,seq(4,(359-7),12)]
+may=tt[,seq(5,(359-6),12)]
+june=tt[,seq(6,(359-5),12)]
+july=tt[,seq(7,(359-4),12)]
+august=tt[,seq(8,(359-3),12)]
+september=tt[,seq(9,(359-2),12)]
+october=tt[,seq(10,(359-1),12)]
+november=tt[,seq(11,359,12)]
+december=tt[,seq(12,359-11,12)]
+
+year=list(january,february,march,april,may,june,july,august,september,october,november,december)
+
+
+
+monthlytemp.frame <- as.data.frame(matrix(,ncol=(36),nrow=0))
+for(i in seq(1,dim(tt)[1])){
+ yeartemp=c()
+ for(mois in seq(1,12)) {
+  month_min=min(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
+  month_max=max(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
+  month_mean=mean(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
+  yeartemp=c(yeartemp,month_min,month_max,month_mean)
+ }
+ monthlytemp.frame=rbind(monthlytemp.frame,yeartemp) 
+}
+
+mois_nom=c("january","february","march","april","may","june","july","august","september","october","november","december")
+value_nom=c("min","max","mean")
+col_nom=c()
+for(m in mois_nom){
+	for(n in value_nom) {
+		mois_value=paste(m,n,sep="_")
+		nom_value=paste("SST",as.character(mois_value),sep="_")
+		col_nom=c(col_nom,as.character(nom_value))
+	}
+}
+colnames(monthlytemp.frame)=col_nom
+
+monthlytemp.coo=cbind(coo,monthlytemp.frame)
+
+write.table(monthlytemp.coo, file="03-results/all_monthly_temperature.tsv",quote=F,sep="\t",col.names=T,row.names=F)
\ No newline at end of file

README.md

@@ -71,6 +71,8 @@ Download the content of /DataEnvironment/resources and copy it into the folder [
 * 01-infos/chlorophyll/surface/Present.Surface.Chlorophyll.Max.tif
 * 01-infos/chlorophyll/surface/Present.Surface.Chlorophyll.Mean.tif
 * 01-infos/chlorophyll/surface/Present.Surface.Chlorophyll.Min.tif
+* 01-infos/salinity/MEDSEA_PHY_006_004_SSS_jan1987-nov2016_monthly.nc
+* 01-infos/temperature/MEDSEA_PHY_006_004_SST_jan1987-nov2016_monthly.nc
 
 # 3. Reporting bugs
 
@@ -97,6 +99,18 @@ Rscript 00-scripts/chlorophyll.R
 
 ```
 
+To attribute "salinity" information (this will generate [03-results/all_monthly_salinity.tsv](03-results/all_monthly_salinity.tsv))
+```
+Rscript 00-scripts/sss.R
+
+```
+
+To attribute "temperature" information (this will generate [03-results/all_monthly_temperature.tsv](03-results/all_monthly_temperature.tsv))
+```
+Rscript 00-scripts/sst.R
+
+```
+
 To merge all data into one single table (this will generate [03-results/all.tsv](03-results/all.tsv))
 ```
 Rscript 00-scripts/merge_table.R
@@ -107,4 +121,6 @@ Rscript 00-scripts/merge_table.R
 
 * [03-results/all_habitat.tsv](03-results/all_habitat.tsv) : table of samples with WGS84 coordinates and predicted habitat
 * [03-results/all_chlorophyll.tsv](03-results/all_chlorophyll.tsv) : table of samples with WGS84 coordinates and chlorophyll A - benthic and surface - mean,max,min values
+* [03-results/all_monthly_salinity.tsv](03-results/all_monthly_salinity.tsv) : table of samples with WGS84 coordinates and monthly salinity - mean,max,min values
+* [03-results/all_monthly_temperature.tsv](03-results/all_monthly_temperature.tsv) : table of samples with WGS84 coordinates and monthly temperature - mean,max,min values
 * [03-results/all.tsv](03-results/all.tsv)  : table of samples with WGS84 coordinates and all the environmental data (predicted habitat, chlorophyll A)